title: 02C_TP_RPL22B

source_name: Transcriptional_Profile_45 fL

value: 45 fL


title: 02A_TP_RPL22B

status: Public on Nov 20 2019

type: SRA

city: College Station

first: Rodolfo

last: Aramayo

state: Texas

address: Room 412, Biological Sciences Building West (BSBW)

department: Biology

country: USA

institute: Texas A&M University

library_source: transcriptomic

data_processing:
Sample libraries were sequenced using the Illumina HiSeq 4000 in High Output mode. Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings. Sequencer .bcl basecall files were de-multiplexed, allowing a 1bp mismatch, and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl. Cutadapt 1.8 was used to identify reads that contained >5bp of sequence adaptor and binned but not processed to remove adaptor.
bowtie-align-s version 1.2.2
RSEM v1.3.1
samtools 1.3
Genome_build: S288C_reference_sequence_R64-2-1_20150113
Supplementary_files_format_and_content: All output files are rsem-calculate-expression output files in text format

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)

extract_protocol:
We used the same approach we had described previously (Blank et al., 2017), to collect cells from elutriated cultures of each ribosomal protein deletion and generate ribosome footprint libraries. For the RNAseq libraries from the same samples, we also used the same approach we had described (Blank et al., 2017), except that we did not select for polyA-tailed RNAs. Instead, from total RNA, we depleted rRNA, using the ‘Ribo-Zero™ Magnetic Gold Kit (Yeast)’, according to the manufacturer’s instructions.
All RNA-seq libraries were sequenced on an Illumina HiSeq4000, with multiplexing, at the Texas A&M AgriLife Genomics and Bioinformatics Facility
For the ribosome footprint libraries, the cell extracts were prepared as follows: The cell pellets were in 1.5 ml screw-cap microcentrifuge tubes and they were washed once with 1 ml ice-cold DEPC-treated water, centrifuged at 13,000 g for 1 min and the supernatant was aspirated. To each tube we added 0.25 ml glass beads (425-600 μm; Sigma-Aldrich, Cat#: G9268) and 0.4 ml ice-cold lysis buffer, which is described in Ingolia et al (Ingolia et al., 2012). The cells were broken by vortexing at full speed eight times, for 15 sec each time. The samples were placed in ice for at least 30 sec between each vortexing. The extracts were clarified by centrifugation at 5,000 g for 5 min, at 4 °C. The supernatant was clarified in a second centrifugation, at 13,000 g for 10 min, at 4 °C.
All subsequent steps for the ribosome footprint libraries were performed as described in Ingolia et al (Ingolia et al., 2012), except step 7, where we used 1.875 μl of RNase I (100 U μl-1) per reaction. For all gel extractions, we used the overnight protocol described in (Ingolia et al., 2012). Depletion of rRNA was done as described in (Ingolia et al., 2012). In the final PCR amplification and barcode addition step, we amplified each library for 12 cycles

treatment_protocol: We used centrifugal elutriation to isolate growing, highly synchronous, unbudded, early G1 cell populations and scored the elutriated cultures over time microscopically, recording the percentage of budded cells with a particle counter that directly measures their volume (channelyzer). Generation of both the Ribosome Profile (RP) and Transcriptional Profile (TP) libraries require at least ≥2E+09 yeast cells per sample. Such sample size could not be collected following a typical time-series experiment because only a small minority of the total cell population is in early G1 at any given moment. Instead, we allowed the entire cell population of each elutriated fraction to progress in the cell cycle until it reached a given cell size (e.g., 40  fL), at which point the sample was harvested. Elutriated cells of the same size were pooled together until enough cells per sample were obtained. This pool of same-size cells defined one experimental replicate (e.g., Sample01A). We harvested cells with 5 fL cell size increments, from the time they are born (40  fL -- Sample01), until the end of the cell cycle (75  fL -- Sample08)

tag: genotype/variation

tag: ploidy

value: diploid

tag: culture condition

tag: timepoint

tag: experiment type

value: Transcriptional Profiling

tag: molecule subtype

value: PolyA RNA


title: 02B_TP_RPL22B

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: 01C_TP_RPL22B

source_name: Transcriptional_Profile_40 fL

value: 40 fL


title: Subject5.W16.NL.Placebo

type: RNA

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

label: biotin

organism: Homo sapiens

source_name: adult with moderate-to-severe atopic dermatitis

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: diagnosis

value: atopic dermatitis

tag: tissue

value: skin

value: NL

tag: treatment

value: Placebo

tag: technique

value: Vivo


title: 01B_TP_RPL22B


title: Hdc_gfphi HSC sample_1

first: Timothy

middle: Cragin

last: Wang

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie2 and Tophat 2.0.4.
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: xlsx file with raw counts for each gene

organism: Mus musculus

source_name: Hdc-GFPhi HSC cells

extract_protocol:
Total RNA was isolated from sorted 500 Hematopoetic Stem Cells using the ARCTURUS PicoPure RNA isolation kit (Life Technologies).
cDNA was amplified using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories),
Libraries were constructed using the Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions.

tag: strain background

value: Hdc-GFPhi

value: bone marrow

tag: cell type

value: hematopoetic stem cells (HSCs)

tag: sorted fraction


title: 01A_TP_RPL22B


title: 08C_RP_RPL22B

source_name: Ribosome_Profile_75 fL

value: 75 fL

value: Ribosome Profiling

value: Protected RNA


title: 08B_RP_RPL22B


title: Subject5.W4.NL.Placebo


title: Subject5.W4.LS.Placebo

value: LS


title: C21_H009

city: wenzhou

first: chenlei

last: zheng

address: wenzhou medical university

country: China

institute: wenzhou medical university

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

organism: Rattus norvegicus

source_name: quadriceps

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Male Sprague-Dawley rats (body weight: 150-200 g) were injected once a day with saline (control) or FK506 in saline (1 mg/kg BW) for 14 days.

value: quadriceps

value: control


title: 07C_RP_RPL22B

source_name: Ribosome_Profile_70 fL

value: diploid

value: 70 fL


title: h1met1_input_dnase_rep3

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

library_source: genomic

data_processing:
Illumina Hiseq basecalls were performed using 'bcl2fq' at the U.C.Berkeley sequencing core facility.
For bisulfite-seq, reads were mapped with bowtie and bs-sequel pipeline (https://zilbermanlab.net/tools/) allowing up to 2 mismatches.
For RNA-seq libraries, reads were mapped with HISAT2 with following options: --max-intronlen 10000 -k 2 --dta. we kept uniquely mapped reads for annotating TE genes and antisense transcripts with StringTie.
For decap-seq libraries, adapter sequences were trimmed using CUTADAPT, leaving reads longer than 20 bp. Adapter-trimmed reads were mapped with HISAT2 with following options: --max-intronlen 10000 -k 2 --dta.
For ChIP- and ChAP-seq, reads were mapped with Bowtie allowing up to 2 mismatches and normalized by RPKM. Log 2 ratio between IP- or AP-ed and input was calculated by bamcompare function in deepTools2.
For DNase-seq read were mapped with Bowtie and normalized by RPKM with a Perl script 'window_alignment' and 'gff_arithmetics' (https://zilbermanlab.net/tools/).
Genome_build: TAIR10
Supplementary_files_format_and_content: For bisulfite-seq, GFF files contain DNA methylation of average 50 bp windows. For other data, bigwig files contain log2 ratio between treated and input sampes

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 2 week old seedlings

growth_protocol: Around 200 seeds were germinated and grown in half strength Gamborg's B5 media for 2-4 weeks under continuous light. h1.1 h1.2 plants (Zemach et al., 2013) were crossed to met1-6 +/- (Xiao et al., 2003) to genenrate h1.1 h1.2 met1-6 triple knockout mutants. After crossing, h1.1 h1.2 met1-6 +/- were isolated at F2 generation, then homozygous triple knockout mutants were indentified at F3. F4 homozygous mutant plants were used for sequencing.

extract_protocol: Arabidopsis nuclei were isolated and re-suspended in NIB as described in ChIP-seq library preparation. After centrifugation at 6,000 rpm for 20 min at 4 C, nuclei pellets were re-suspended in 400 ml DNaseI buffer (10 mM Tris-HCl pH 8.0, 2.5 mM MgCl2, 0.5 mM CaCl2). 100 ml of nuclei was incubated with 0.1-2 U / ml DNase I (New England Biolabs, cat. No. M03030S) for 3 min at 37 C. 50 mM EDTA, 0.5 % SDS (final concentration), 2 ml proteinase K were added and incubated at 55 C for 1 hr to stop digestion. To completely denature chromatin, more SDS were added to make final 1% concentration then incubated at 65 C for 15 min. gDNA were isolated with P:C:I and DNA fragmentation were visualized by DNA electrophoresis. Samples with similar degree of DNA digestion were selected to construct library. 0.5 X volume of SPRI beads were added to remove undigested gDNA. Supernatant were collected and purified with 1.25 X volume of SPRI beads.

value: 2 week old seedlings


title: h1met1_input_dnase_rep2


title: Subject5.W0.NL.Placebo

value: atopic dermatitis


title: h1met1_input_dnase_rep1


title: 07B_RP_RPL22B

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: 07A_RP_RPL22B


title: S3_H004

value: model


title: 06B_RP_RPL22B

source_name: Ribosome_Profile_65 fL

value: 65 fL


title: S2_H003


title: C3_H001


title: C1_H002


title: 06A_RP_RPL22B


title: Subject4.W4.LS.Stelara

value: skin

value: Ustekinumab

value: Vivo


title: M2_H005


title: Subject5.W0.LS.Placebo

value: Placebo


title: Subject4.W0.LS.Stelara


title: 08A_RP_RPL22B

value: 75 fL


title: 06C_RP_RPL22B

value: Ribosome Profiling


title: met1_input_dnase_rep2


title: 05A_RP_RPL22B

source_name: Ribosome_Profile_60 fL

value: 60 fL

value: Protected RNA


title: met1_input_dnase_rep1


title: 05B_RP_RPL22B


title: 04C_RP_RPL22B

source_name: Ribosome_Profile_55 fL

value: 55 fL


title: Subject3.W20.LS.Placebo

value: LS


title: h1_input_dnase_rep3


title: 04A_RP_RPL22B

value: diploid


title: met1_input_dnase_rep3


title: 03B_RP_RPL22B

source_name: Ribosome_Profile_50 fL

value: 50 fL


title: 05C_RP_RPL22B


title: Subject3.W16.NL.Placebo

value: NL


title: 03C_RP_RPL22B


title: Subject3.W4.LS.Placebo

value: atopic dermatitis


title: Subject4.W0.NL.Stelara


title: h1_input_dnase_rep1

value: 2 week old seedlings


title: Subject3.W16.LS.Placebo


title: Subject3.W0.LS.Placebo


title: 02C_RP_RPL22B

source_name: Ribosome_Profile_45 fL

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)

value: 45 fL


title: 02B_RP_RPL22B


title: wt_input_dnase_rep5


title: wt_input_dnase_rep4


title: 03A_RP_RPL22B


title: 01C_RP_RPL22B

source_name: Ribosome_Profile_40 fL

value: 40 fL


title: 02A_RP_RPL22B


title: 04B_RP_RPL22B


title: 01A_RP_RPL22B


title: 01B_RP_RPL22B


title: wt_input_dnase_rep3


title: GFP alone GFP-alone

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

description:
GFP alone
total RNA
GFP-alone.bw

data_processing:
The raw data of CB-RNA were mapped to Arabidopsis genome (TAIR10) with hisat2 v2.0.5, and FPKM of the genes were calculated by stringtie v1.3.4d with default parameters.
Genes with FPKM <1 were filtred in following 5'SS or 3'SS ratio calculation for exon-intron-exon to determine co-transcription splicing frequency. We counted reads from CB-RNA-seq mapped to 25 bp upstream (5' exonic reads) or downstream (5' intronic reads) of exon-intron junction as well as 25 bp downstream (3' exonic reads) or upstream (3' intronic reads) of intron-exon junction. We calcuated the ratio of 5' intronic reads number to 5' exonic reads number as 5' SS value. 3' SS value was calculated in similar way. The differentially splicing introns between the wild type and the double mutant were identified using Fisher test. Briefing, Fisher test was performed via the normalized CB-RNA-seq read counts of each intron and its two flanking exons of WT and rz-1b rz-1c, following by BH multiple comparison correction. The intron with FDR less than 0.001 was considered as the differentially splicing intron.
The raw data of mRNA-seq were mapped with tophat v2.1.1. Cufflinks v2.2.1was used to calculate FPKM of genes. Cuffdiff v2.2.1 was used to identify significant differentially expressed genes with criteria FPKM > 1, the fold change > 2 and FDR < 0.05.
iCLIP data were processed using iCount v2.0.1.dev. Paired-end sequencing data were generated in this study, however only 3’end sequencing reads should be used in binding sites identification based on process of iCLIP experiment. In brief, we used “demultiplex”function removed the adapter of reads and extracted 10 bp randomer sequences. Then the cleaning reads were aligned with “Mapstar” function. All binding sites were identified and quantified using "Xlsites" function (parameters: --group_by start--quant cDNA). Finally, "peaks" function was used to identify significantly binding sites (FDR<0.05), and binding clusters were generated with "clusters" function.
For 5 replicates generated by iCLIP, the clusters were identified in each replicate and in data that pooled replicates together, respectively. Only clusters of pooled replicates that were identified in all 5 replicates as well were retained as binding clusters. Only binding sites in the binding clusters were kept in following analysis. And MEME-chip was used to find motifs of the binding clusters.
Genome_build: Tair10 Arabidopsis genome
Supplementary_files_format_and_content: Processed data were stored in excel files, which included differentially expression genes from  wild type and mutant of Arabidopsis thaliana.

source_name: GFP-alone iCLIP

growth_protocol: Seedling were grown on 1/2 Murashige and Skoog (MS) medium for 10 days at 22 °C under 16hr light/ 8hrs dark cycles.

extract_protocol:
CB-RNA-seq : Nuclei from 2g of grinded powder of seedlings were prepared by using Honda buffer supplement with RNase inhibitor and yeast tRNA to protect the integrity of RNA. The nuclei pellet was first resuspended in an equal volume of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 1 mM DTT, 25 mM Tris-HCL pH 7.5, 100 mM NaCl, 100ng/ul tRNA, 0.01U/ul RNase In), followed by brief washing with two volumes of UREA wash buffer (25 mM Tris-HCL pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1 mM DTT, 1% Tween-20). The chromatin was pelleted by centrifuge at 8000g for 1mins, resuspension with equal volume of resuspension buffer, followed by washing by using 1 volume of UREA buffer. The resulting chromatin pellet after centrifugation was resuspended in 1mL Trizol and followed by RNA extraction in combination with RNeasy Mini Kit (Qiagen).  The integrity of resulting CB-RNA was checked on gel by comparing to the pattern of total RNA.  DNA leftover was removed from CB-RNA by two sequential digestions with Turbo DNase (Thermo).  The resulting RNA were then used for further analysis of the enrichment of nascent RNA (qPCR) and constructing the RNA-seq library. iCLIP-seq : Plant growing on petri-dish for 10 days were immersed in an sallow layer of cold 1xPBS and cross-link with UV light at 600mJ/cm once. 2g of N2 grinded plant powers were lysed with lysis buffer, DNase RNase treated and sonicated to release the RNA/proteins. The resulting lysate were cleared with centrifugation, subject to immunoprecipitation with anti-GFP antibody (Ab290, Abcam) and protein A (Dynabeads, Thermo).
CB-RNA-seq library: CB-RNA was treated with Ribozero (Illumina) to remove the rRNA following the kit instruction. Leftover polyA RNAs were also removed by using Oligo d(T) cellulose beads (NEB). Strand specific RNA-seq library were then constructed by using dUTP method. iCLIP-seq library: The RNA/protein complex after IP were washed extensively including several wash with high salt wash buffer, treated with PNK and Alkinine phosphatase to remove the terminal phosphate, ligated to RNA adaptor at 3’end and end labeled with p32.  90% of the resulting complex were eluted by LDS sample buffer and resolved on 4-12% NuPAGE gel, transfer to nitrocellulose membrane for autoradiograph.  The rest 10% of the complex were run in parallel to check the enrichment of target protein.  The region above the size of proteins were cutted out based on the autoradiograph,  RNA were released by proteinase K digestion.  The resulting RNA was further purified and reverse transcribed by Superscript III (Thermo) using primer complement to the RNA adaptor.  The resulting cDNA were purified and subject to adaptor ligation to its 3’end.  The final library was amplified by using primers specific to both end adaptors from cDNA by Q5 hotstart DNA polymerase. For Input sample, the supernatant after cell lysis were treated the same as iCLIP procedure as described above except the IP were omitted. The resulting PCR product were resolved on 6% native PAGE gel and fragment from 175-400bp were recovered from gel and send for pair-end illumina (PE150) sequencing.

value: seedlings


title: 08C_TP_RPL22A

source_name: Transcriptional_Profile_75 fL

value: Transcriptional Profiling

value: PolyA RNA


title: Subject3.W0.NL.Placebo

value: skin

value: Placebo

value: Vivo


title: Subject2.W4.LS.Stelara

value: Ustekinumab


title: 08B_TP_RPL22A

value: 75 fL


title: Subject2.W0.LS.Stelara

value: LS


title: wt_input_dnase_rep2


title: 07C_TP_RPL22A

source_name: Transcriptional_Profile_70 fL

value: diploid

value: 70 fL


title: Subject2.W0.NL.Stelara

value: NL


title: wt_input_dnase_rep1


title: 07B_TP_RPL22A


title: 07A_TP_RPL22A


title: RZ-1C iCLIP replicate 4 RZ-1C-iCLIP-4

description:
RZ-1C iCLIP replicate 4
total RNA
RZ-1-GFP.bw

source_name: RZ-1C-GFP iCLIP


title: 08A_TP_RPL22A


title: RZ-1C iCLIP replicate 3 RZ-1C-iCLIP-3

description:
RZ-1C iCLIP replicate 3
total RNA
RZ-1-GFP.bw


title: RZ-1C iCLIP replicate 2 RZ-1C-iCLIP-2

description:
RZ-1C iCLIP replicate 2
total RNA
RZ-1-GFP.bw


title: 06C_TP_RPL22A

source_name: Transcriptional_Profile_65 fL

value: 65 fL


title: h1met1_dnase_rep3

description: processed_data_file: h1met1.dnase.w50.bw

value: 2 week old seedlings


title: h1met1_dnase_rep1


title: 06B_TP_RPL22A

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: 05C_TP_RPL22A

source_name: Transcriptional_Profile_60 fL

value: 60 fL


title: 06A_TP_RPL22A


title: met1_dnase_rep3

description: processed_data_file: met1.dnase.w50.bw


title: 05B_TP_RPL22A


title: RZ-1C iCLIP replicate 1 RZ-1C-iCLIP-1

description:
RZ-1C iCLIP replicate 1
total RNA
RZ-1-GFP.bw


title: RZ-1C iCLIP replicate 5 RZ-1C-iCLIP-5

description:
RZ-1C iCLIP replicate 5
total RNA
RZ-1-GFP.bw


title: rz−1b rz−1c replicate 3 mutant-2-1

description:
rz−1b rz−1c replicate 3
mRNA
WT_VS_mutant_DEGs.xlsx

source_name: mRNA of  mutant


title: met1_dnase_rep2

description: processed_data_file: met1.dnase.w50.bw


title: 04C_TP_RPL22A

source_name: Transcriptional_Profile_55 fL

value: 55 fL


title: 04B_TP_RPL22A


title: rz−1b rz−1c replicate 2 mutant-1-2

description:
rz−1b rz−1c replicate 2
mRNA
WT_VS_mutant_DEGs.xlsx

value: seedlings


title: met1_dnase_rep1

description: processed_data_file: met1.dnase.w50.bw


title: 04A_TP_RPL22A

value: Transcriptional Profiling


title: 03C_TP_RPL22A

source_name: Transcriptional_Profile_50 fL

value: 50 fL

value: PolyA RNA


title: rz−1b rz−1c replicate 1 mutant-1-1

description:
rz−1b rz−1c replicate 1
mRNA
WT_VS_mutant_DEGs.xlsx


title: h1met1_dnase_rep2


title: h1_dnase_rep3

description: processed_data_file: h1.dnase.w50.bw


title: Col-0 replicate 3 WT-2-1

description:
Col-0 replicate 3
mRNA
WT_VS_mutant_DEGs.xlsx

source_name: mRNA of  Col-0


title: h1_dnase_rep2

description: processed_data_file: h1.dnase.w50.bw

source_name: 2 week old seedlings


title: Col-0 replicate 2 WT-1-2

description:
Col-0 replicate 2
mRNA
WT_VS_mutant_DEGs.xlsx


title: Col-0 replicate 1 WT-1-1

description:
Col-0 replicate 1
mRNA
WT_VS_mutant_DEGs.xlsx


title: 03B_TP_RPL22A


title: wt_dnase_rep5

description: processed_data_file: col.dnase.w50.bw


title: rz−1b rz−1c replicate 2 mutant-CB-2-2

description:
rz−1b rz−1c replicate 2
chromatin-bound RNA
mutantCB-FPKM.xlsx

source_name: chromatin-bound RNA of mutant


title: BTB2_T12

first: Tharu

middle: M

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

description:
WT_mutBTB_allrawcounts.txt
topTags_mutBTB_mouse_humangeneid_cpm-3_FDR0.05.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads that passed filter were aligned to mm10 using STAR (Dobin et al., 2012).
Gene expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/HTSeq/).
Differentially expressed genes were identified with the edgeR package (Robinson et al., 2010).  Genes with a logCPM < -3 and FDR < 0.05 were considered differentially expressed.
Biomart was used to find convert mouse gene IDs to human gene IDs.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count is provided as a .txt file.

source_name: Splenic B220+ cells

growth_protocol: Cells were grown in RPMI 1640 medium with 10% FBS, 10 mM Hepes, 2 mM glutamine, and pen/strep.

extract_protocol:
Total RNA was harvested with Trizol reagent (Life Technologies).
Genomic DNA was eliminated with Dnase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.

treatment_protocol: Cells were harvested at time 0 (T0) or heat shocked at 39 C for 1 h and returned to 37 C for 12 h (T12).

tag: strain

value: 39 C for 1 h, followed by 37C for 12 h


title: BTB1_T0


title: 05A_TP_RPL22A


title: BTB1_T12


title: 02C_TP_RPL22A

source_name: Transcriptional_Profile_45 fL

value: 45 fL


title: BTB2_T0


title: 02A_TP_RPL22A


title: 01C_TP_RPL22A

source_name: Transcriptional_Profile_40 fL

value: 40 fL


title: 02B_TP_RPL22A


title: wt_dnase_rep4

description: processed_data_file: col.dnase.w50.bw


title: rz−1b rz−1c replicate 2 mutant-CB-2-1


title: WT2_T12

description:
WT_mutBTB_allrawcounts.txt
topTags_WT_mouse_humangeneid_cpm-3_FDR0.05.txt

value: wild-type


title: wt_dnase_rep3

description: processed_data_file: col.dnase.w50.bw


title: 01B_TP_RPL22A


title: wt_dnase_rep2

description: processed_data_file: col.dnase.w50.bw


title: WT1_T12


title: 01A_TP_RPL22A


title: 03A_TP_RPL22A


title: WT2_T0


title: wt_dnase_rep1

description: processed_data_file: col.dnase.w50.bw


title: h1_dnase_rep1

description: processed_data_file: h1.dnase.w50.bw


title: 08C_RP_RPL22A

source_name: Ribosome_Profile_75 fL

value: 75 fL

value: Ribosome Profiling

value: Protected RNA


title: WT1_T0


title: Col-0 replicate 2 WT-CB-2-2

description:
Col-0 replicate 2
chromatin-bound RNA
WTCB-FPKM.xlsx

source_name: chromatin-bound RNA of Col -0


title: met1_input_ChIP

extract_protocol: 2 g of 2-weeks-old seedlings were cross-linked with 32 ml of crosslinking buffer (0.4 M sucrose, 10 mM tris-HCl pH 8.0, 1 mM EDTA and 1% formaldehyde (Thermo Scientific, cat. No. 28906)) for 10 min under vacuum. Cross-linking was quenched by applying vacuum for 5 min with 2 ml 2 M glycine. Cross-linked seedlings were washed with distilled water, pat dried with paper towels, frozen and ground in liquid nitrogen with pestle and mortar. Ground tissues were re-suspended in 20 ml of nuclei isolation buffer at 4 C (NIB; 0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1X complete EDTA-free protease inhibitor cocktail (Roche, cat. No. 11873580001)). Homogenized slurry was filtered through Miracloth (Millipore, cat. No. 475855) and centrifuged at 6,000 rpm for 20 min at 4 C to pull-down nuclei. After discarding supernatant, cell pellets were re-suspended in 1ml 4 C nuclei lysis buffer (NLB; 50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 % SDS, 1 % Triton X-100, 1X complete EDTA-free protease inhibitor). 500 ml nuclei solution was sonicated and centrifuged for 10 min at 13,000 rpm in table-top centrifuge (4 C). Sonicated chromatin in supernatant was transferred and diluted 5 times with dilution buffer (NLB without SDS and Triton X-100). 200 ml of diluted chromatin was incubated with 7 ml of antibodies against H3K9me2 (Abcam, cat. No. AB1220) overnight with rotation at 4 C. 45 ml of pre-cleared protein G dynabeads (Invitrogen, 10003D) were added and incubated for 4 hours with rotation at 4 C. 20 ml of diluted chromatin solution was kept for input control. Chromatin bound to the antibodies were washed 4 times with low salt wash buffer (150 mM NaCl, 20 mM Tris-HCl pH 8.0, 0.2% SDS, 0.5% Triton X-100, 2 mM EDTA) and one time with TE buffer (1 mM EDTA and 10 mM Tris-HCl pH 8.0) at 4 C. Washed chromatin were re-suspended in 200 ml elution buffer (1% SDS), and incubated at 65 C for 5 hrs with 8 ml of 5M NaCl (vortex for 1 hr). To digest proteins bound to gDNA, samples were incubated 1 hr at 55 C with 4 ml proteinase K (Thermo, cat. No. EO0492), 4 ml of 0.5 M EDTA, 8 ml of 1 M tris-HCl pH 8. After reverse-crosslinking, 220 ml P:C:I, 500 ml ethanol, 20 ml 3M sodium acetate (pH 5.2), and 2 ml glycogen were added and incubated overnight at -80 C to extract DNA.


title: wt_input_ChIP


title: 08B_RP_RPL22A

value: diploid


title: 08A_RP_RPL22A


title: Col-0 replicate 2 WT-CB-2-1


title: Col-0 replicate 1 WT-CB-1-2

description:
Col-0 replicate 1
chromatin-bound RNA
WTCB-FPKM.xlsx


title: 07C_RP_RPL22A

source_name: Ribosome_Profile_70 fL

value: 70 fL


title: h1met1_hetero_decap_rep3

description:
decap_h1met1_hetero.f.bw
decap_h1met1_hetero.r.bw

source_name: leaf tissue

extract_protocol:
10 mg of RNA was subjected to DNA-free DNA removal kit (Thermo, AM1907) to degrade DNA from samples. To remove rRNA, RNA was treated with RiboMinus Plant Kit for RNA-Seq (Invitrogen, A1083808). rRNA-depleted total RNA was chemically fragmented, then dephhorylated using Antarctic phosphatase (NEB, M0289).  5' cap of RNA was removed by incubating with RNA 5' pyrophosphohydrolase (RppH, NEB M0356) in 1X Thermopol buffer (NEB B9004S). DECAP-seq libraries were constructed using TruSeq small RNA library prep kit (Illumina, RS-200-0012). To prevent 21- or 24-nt sRNA contamination, library fragments larger than 180 bp were selected for sequencing.
To construct bisulfite sequencing libraries, about 500 ng of purified gDNA was fragmented to roughly 100-1000 bp then purified using 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was end-repaired and ligated to HPLC/PAGE purified, cytosine-methylated Illumina adapters (Elim Biopharmaceuticals, Inc.). DNA was subjected to two rounds of bisulfite conversion according to manufacturer's protocol (Qiagen, cat. No. 59104). To remove self-ligated adapters, DNA was purified twice with 0.8X volume of SPRI beads. NEB next indexing primers were used to amplify bisulfite-converted libraries (New England BIolabs Inc. cat. No. E7335S). DNA fragments isolated for ChIP-, ChAP-, and DnaseI-sequencing were subjected to Illumina library construction as described in bisulfite sequencing library construction except for the two rounds of bisulfite conversion.


title: h1met1_hetero_decap_rep2


title: rz−1b rz−1c replicate 1 mutant-CB-1-2

description:
rz−1b rz−1c replicate 1
chromatin-bound RNA
mutantCB-FPKM.xlsx


title: met1_H3K9me2_ChIP

description: processed_data_file: met1.H3K9me2.w50.bw

value: 2 week old seedlings


title: h1met1_hetero_decap_rep1


title: 07B_RP_RPL22A

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: 07A_RP_RPL22A


title: rz−1b rz−1c replicate 1 mutant-CB-1-1


title: h1met1_hetero_decap_rep4


title: 06C_RP_RPL22A

source_name: Ribosome_Profile_65 fL

value: 65 fL


title: 4384 Seed train rep3 (dataset 2)

city: Canterbury

first: Davide

last: Vito

state: Kent

address: Ingram Building, University of Kent

institute: University of Kent

description: 4384 Seed train rep3

data_processing:
Sequenced reads were trimmed for adaptor and low-quality sequence with Trim_Galore!, then mapped to GCF_000419365.1 with STAR with parameters cut -c 36
Gene counts in exonic regions were calculated using featureCounts, then expressed in Reads Per Kilobase of exon per Megabase of library size (RPKM) with an R script
Genome_build: GCF_000419365.1
Supplementary_files_format_and_content: CSV text files include RPKM values for each sample

organism: Cricetulus griseus

source_name: CHO suspension culture

extract_protocol:
Cells were pelleted and lysate with TRI-Reagent, followed by Direct-zol RNA kit for RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: day


title: 4384 Seed train rep2 (dataset 2)

description: 4384 Seed train rep2


title: wt_input_ChAP

source_name: 4 week old roots

extract_protocol: ChAP experiments were performed according to previous publication with minor modifications (Zilberman et al. 2008)ChAP experiments were performed according to previous publication with minor modifications (Zilberman et al. 2008).4-week-old roots were vacuum infiltrated in 1% formaldehyde solution for 15 minutes to cross-link the chromatin. Roots were ground in liquid nitrogen and nuclei were isolated as described (Zilberman et al. 2008). The nuclear suspension was fragmented by sonication to 0.5-2 kb then 90% of biotinylated protein-containing chromatin was affinity purified using streptavidin beads. 10% of the sheared chromatin suspension was used as input control. Reverse cross-linking was performed with 5M NaCl and the DNA was purified as described (Zilberman et al. 2008)..4-week-old roots were vacuum infiltrated in 1% formaldehyde solution for 15 minutes to cross-link the chromatin. Roots were ground in liquid nitrogen and nuclei were isolated as described (Zilberman et al. 2008). The nuclear suspension was fragmented by sonication to 0.5-2 kb  then 90% of biotinylated protein-containing chromatin was affinity purified using streptavidin beads. 10% of the sheared chromatin suspension was used as input control. Reverse cross-linking was performed with 5M NaCl

value: 4 week old roots


title: met1_H1.2_ChAP

description: processed_data_file: met1.H1.2.w50.bw


title: h1met1_decap_rep12

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: wt_H3K9me2_ChIP

description: processed_data_file: col.H3K9me2.w50.bw


title: 06B_RP_RPL22A


title: 4384 Seed train rep1 (dataset 2)

description: 4384 Seed train rep1


title: h1met1_decap_rep11

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: met1_H1.1_ChAP

description: processed_data_file: met1.H1.1.w50.bw


title: 4384 Day 7 rep3 (dataset 2)

description: 4384 Day 7 rep3


title: Col-0 replicate 1 WT-CB-1-1

value: seedlings


title: 4384 Day 7 rep1 (dataset 2)

description: 4384 Day 7 rep1


title: wt_H1.2_ChAP

description: processed_data_file: col.H1.2.w50.bw


title: met1_input_ChAP


title: 4384 Day 7 rep2 (dataset 2)

description: 4384 Day 7 rep2


title: h1met1_decap_rep10

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: 05C_RP_RPL22A

source_name: Ribosome_Profile_60 fL

value: 60 fL


title: wt_H1.1_ChAP

description: processed_data_file: col.H1.1.w50.bw


title: 06A_RP_RPL22A


title: h1met1_decap_rep8

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: 05B_RP_RPL22A


title: S16_mTECs

city: Montreal

first: Krystel

last: Vincent

state: Quebec

address: 2950, chemin de la Polytechnique, Marcelle-Coutu Pavilion

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11
Samples demultiplexed using bcl2fastq 2.20
Sequenced reads were trimmed for sequencing adapters and low quality extrimities using Trimmomatic 0.35 and then mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 26
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

molecule: polyA RNA

source_name: medullary thymic epithelial cells

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA Stranded PolyA

value: medullary thymic epithelial cells (mTECs)


title: h1met1_decap_rep9

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: h1met1_decap_rep13

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: 4384 Day 4 rep2 (dataset 2)

description: 4384 Day 4 rep2


title: 05A_RP_RPL22A


title: S15_mTECs


title: 4384 Day 4 rep1 (dataset 2)

description: 4384 Day 4 rep1


title: h1met1_decap_rep7

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: S9_medullary thymic epithelial cells

data_processing:
Basecalls performed using Illumina RTA 1.18.64
Samples demultiplexed using bcl2fastq 2.17
Sequenced reads were trimmed for sequencing adapters and low quality extrimities using Trimmomatic 0.35 and then mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 26
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

extract_protocol: KAPA RNA Stranded PolyA

tag: extract protocol

value: TriZol + RNeasy mini Kit (Qiagen, #74106)


title: h1met1_decap_rep6

description:
decap_h1met1.f.bw
decap_h1met1.r.bw

tag: genotype/variation


title: 04B_RP_RPL22A

source_name: Ribosome_Profile_55 fL

tag: ploidy

value: 55 fL


title: 3936 Seed train rep3 (dataset 2)

description: 3936 Seed train rep3


title: S5_medullary thymic epithelial cells


title: h1met1_decap_rep5

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: 4384 Day 4 rep3 (dataset 2)

description: 4384 Day 4 rep3


title: 04A_RP_RPL22A

tag: culture condition


title: 3936 Seed train rep2 (dataset 2)

description: 3936 Seed train rep2


title: S11_medullary thymic epithelial cells


title: 3936 Seed train rep1 (dataset 2)

description: 3936 Seed train rep1


title: 03C_RP_RPL22A

source_name: Ribosome_Profile_50 fL

tag: timepoint

value: 50 fL


title: 3936 Day 7 rep3 (dataset 2)

description: 3936 Day 7 rep3


title: h1met1_decap_rep3

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: h1met1_decap_rep2

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: S10_medullary thymic epithelial cells


title: 102015_thymic epithelial cells

source_name: thymic epithelial cells

value: thymic epithelial cells (TECs)

value: TriZol + RNeasy kit


title: 03A_RP_RPL22A

tag: experiment type


title: 3936 Day 7 rep2 (dataset 2)

description: 3936 Day 7 rep2


title: 03B_RP_RPL22A

tag: molecule subtype


title: 04C_RP_RPL22A


title: 02C_RP_RPL22A

source_name: Ribosome_Profile_45 fL

value: 45 fL


title: 3936 Day 7 rep1 (dataset 2)

description: 3936 Day 7 rep1


title: h1met1_decap_rep1

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: 02B_RP_RPL22A

value: Ribosome Profiling


title: 3936 Day 4 rep3 (dataset 2)

description: 3936 Day 4 rep3


title: met1_decap_rep9

description:
decap_met1.f.bw
decap_met1.r.bw


title: 062015_thymic epithelial cells


title: met1_decap_rep8

description:
decap_met1.f.bw
decap_met1.r.bw


title: 3936 Day 4 rep1 (dataset 2)

description: 3936 Day 4 rep1


title: h1met1_decap_rep4

description:
decap_h1met1.f.bw
decap_h1met1.r.bw


title: 01C_RP_RPL22A

source_name: Ribosome_Profile_40 fL

value: 40 fL

value: Protected RNA


title: 02A_RP_RPL22A

value: diploid


title: whole_myofiber_from_young_mouse_WM_3

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

institute: McGill University

data_processing:
Illumina BaseSpace software was used for basecalling.
fastq files were mapped using hisat2 using a index that comes the GRCm38/mm10 genome and ENSEMBL transcriptome (“grcm38_tran” downloaded from the hisat2 website); mapping used default parameters; this resulted in sam files
sam files were converted to bam, sorted and indexed using samtools
Indexed bam files were counted using featureCounts and ENSEMBL gene definitions (“Mus_musculus.GRCm38.97.gtf” obtained from ENSEMBL website), producing ReadCounts.csv
Genome_build: GRCm38/mm110
Supplementary_files_format_and_content: ReadCounts.csv has gene ids on rows, the twelve samples on columns, and reports read counts in a comma-separated text file

source_name: Extensor digitorum longus myofibers

extract_protocol:
RNA was extracted from myofibers using SMART-Seq reaction buffer in RNAse free water
RNA libraries were prepared using the Illumina protocol

tag: tag

value: whole myofiber from young mouse


title: whole_myofiber_from_young_mouse_WM_2


title: met1_decap_rep7

description:
decap_met1.f.bw
decap_met1.r.bw


title: twenty_myofiber_from_young_mouse_F20_3

value: twenty myofiber from young mouse


title: 3080 Seed train rep3 (dataset 2)

description: 3080 Seed train rep3


title: met1_decap_rep6

description:
decap_met1.f.bw
decap_met1.r.bw


title: 01B_RP_RPL22A

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: twenty_myofiber_from_young_mouse_F20_2


title: 01A_RP_RPL22A


title: 3080 Seed train rep1 (dataset 2)

description: 3080 Seed train rep1


title: twenty_myofiber_from_young_mouse_F20_1


title: met1_decap_rep4

description:
decap_met1.f.bw
decap_met1.r.bw


title: 3080 Day 7 rep3 (dataset 2)

description: 3080 Day 7 rep3


title: whole_myofiber_from_young_mouse_WM_1


title: 3936 Day 4 rep2 (dataset 2)

description: 3936 Day 4 rep2


title: met1_decap_rep3

description:
decap_met1.f.bw
decap_met1.r.bw


title: five_myofiber_from_young_mouse_F5_2

value: five myofiber from young mouse


title: five_myofiber_from_young_mouse_F5_1


title: 3080 Day 7 rep1 (dataset 2)

description: 3080 Day 7 rep1


title: 3080 Day 7 rep2 (dataset 2)

description: 3080 Day 7 rep2


title: single_myofiber_from_young_mouse_F1_3

data_processing:
Illumina BaseSpace software was used for basecalling.
Sequenced reads were mapped to mm10 whole genome using hisat2 (v 2.1.0).
htseq-counts (v 0.11.2) (non stranded option) was used with Gencode.vM23 annotation to obtain reads mapped to genes in mm10.
Count tables from htseq-counts, were used by Deseq2 (v 1.24.0) to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files have read counts for genes in mm10, csv file has differentially expressed genes identified by deseq2

source_name: single myofiber from young mouse

extract_protocol:
RNA was extracted from single myofibers using SMART-Seq reaction buffer in RNAse free water
RNA libraries were prepared using the Illumina protocol

tag: age

value: young (4 weeks)

tag: tissue

value: Extensor digitorum longus myofibers


title: 3080 Day 4 rep3 (dataset 2)

description: 3080 Day 4 rep3


title: met1_decap_rep2

description:
decap_met1.f.bw
decap_met1.r.bw


title: wt_decap_rep8

description:
decap_col.f.bw
decap_col.r.bw

value: wild type


title: 3080 Day 4 rep2 (dataset 2)

description: 3080 Day 4 rep2


title: wt_decap_rep7

description:
decap_col.f.bw
decap_col.r.bw


title: NL131

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

description: Patient 13

hyb_protocol: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.qiagen.com/us/products/discovery-and-translational-research/pcr-qpcr/qpcr-assays-and-instruments/mirna-qpcr-assay-and-panels/mircury-lna-mirna-focus-pcr-panels/

scan_protocol: For the normalization it uses the controls: UniSp6, UniSp3, celmiR39-3p, UniSp2, UniSp4, UniSp5.

data_processing:
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: LNA

source_name: miRNAs from urinary exosome

label_protocol: PCR assays were performed using miRCURY LNA™ Universal RT microRNA PCR (Exiqon)

extract_protocol: Total RNA was extracted with miRCURY™ Exosomes Isolation Kit – Cells, urine and CSF

tag: time point

value: Pre-treatment

tag: group

value: Clinical Response


title: NL132

description: Patient 13

value: Post-treatment


title: wt_decap_rep6

description:
decap_col.f.bw
decap_col.r.bw


title: NL122

description: Patient 12


title: NL141

description: Patient 14


title: NL121

description: Patient 12


title: 3068 Seed train rep3 (dataset 2)

description: 3068 Seed train rep3


title: 3080 Day 4 rep1 (dataset 2)

description: 3080 Day 4 rep1


title: single_myofiber_from_young_mouse_SF12


title: met1_decap_rep1

description:
decap_met1.f.bw
decap_met1.r.bw


title: single_myofiber_from_young_mouse_SF21


title: met1_decap_rep5

description:
decap_met1.f.bw
decap_met1.r.bw


title: met1_decap_rep10

description:
decap_met1.f.bw
decap_met1.r.bw


title: five_myofiber_from_young_mouse_F5_3


title: 3080 Seed train rep2 (dataset 2)

description: 3080 Seed train rep2


title: wt_decap_rep4

description:
decap_col.f.bw
decap_col.r.bw

extract_protocol:
10 mg of RNA was subjected to DNA-free DNA removal kit (Thermo, AM1907) to degrade DNA from samples. To remove rRNA, RNA was treated with RiboMinus Plant Kit for RNA-Seq (Invitrogen, A1083808). rRNA-depleted total RNA was chemically fragmented, then dephosphorylated using Antarctic phosphatase (NEB, M0289).  5' cap of RNA was removed by incubating with RNA 5' pyrophosphohydrolase (RppH, NEB M0356) in 1X Thermopol buffer (NEB B9004S). DECAP-seq libraries were constructed using TruSeq small RNA library prep kit (Illumina, RS-200-0012). To prevent 21- or 24-nt sRNA contamination, library fragments larger than 180 bp were selected for sequencing.
To construct bisulfite sequencing libraries, about 500 ng of purified gDNA was fragmented to roughly 100-1000 bp then purified using 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was end-repaired and ligated to HPLC/PAGE purified, cytosine-methylated Illumina adapters (Elim Biopharmaceuticals, Inc.). DNA was subjected to two rounds of bisulfite conversion according to manufacturer's protocol (Qiagen, cat. No. 59104). To remove self-ligated adapters, DNA was purified twice with 0.8X volume of SPRI beads. NEB next indexing primers were used to amplify bisulfite-converted libraries (New England BIolabs Inc. cat. No. E7335S). DNA fragments isolated for ChIP-, ChAP-, and DnaseI-sequencing were subjected to Illumina library construction as described in bisulfite sequencing library construction except for the two rounds of bisulfite conversion.


title: 3068 Seed train rep1 (dataset 2)

description: 3068 Seed train rep1


title: wt_decap_rep3

description:
decap_col.f.bw
decap_col.r.bw


title: single_myofiber_from_old_mouse_SFR1

source_name: single myofiber from old mouse

value: old (19 months)


title: single_myofiber_from_young_mouse_F1_1


title: wt_decap_rep2

description:
decap_col.f.bw
decap_col.r.bw


title: NL102

description: Patient 10


title: single_myofiber_from_old_mouse_SFN2


title: NL112

description: Patient 11


title: single_myofiber_from_old_mouse_SFL2


title: NL092

description: Patient 9


title: 3068 Day 7 rep3 (dataset 2)

description: 3068 Day 7 rep3


title: 3068 Day 7 rep2 (dataset 2)

description: 3068 Day 7 rep2


title: 3068 Day 7 rep1 (dataset 2)

description: 3068 Day 7 rep1


title: wt_decap_rep1

description:
decap_col.f.bw
decap_col.r.bw


title: NL091

description: Patient 9


title: h1met1_hetero_bisulfite

source_name: 2 week old seedlings

extract_protocol:
gDNA for bisulfite sequencing was extracted with Dneasy plant mini kit according to manufacturer's protocol.
To construct bisulfite sequencing libraries, about 500 ng of purified gDNA was fragmented to roughly 100-1000 bp then purified using 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was end-repaired and ligated to HPLC/PAGE purified, cytosine-methylated Illumina adapters (Elim Biopharmaceuticals, Inc.). DNA was subjected to two rounds of bisulfite conversion according to manufacturer's protocol (Qiagen, cat. No. 59104). To remove self-ligated adapters, DNA was purified twice with 0.8X volume of SPRI beads. NEB next indexing primers were used to amplify bisulfite-converted libraries (New England BIolabs Inc. cat. No. E7335S). DNA fragments isolated for ChIP-, ChAP-, and DnaseI-sequencing were subjected to Illumina library construction as described in bisulfite sequencing library construction except for the two rounds of bisulfite conversion.


title: 3068 Day 4 rep3 (dataset 2)

description: 3068 Day 4 rep3


title: NPC-M4

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

description: age-matched non-pregnant female mice

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20.
Sequenced reads were trimmed for sequencing adapters and low quality extremities using Trimmomatic 0.35 and then mapped to the reference genome using STAR version 2.5.1b, guided by transcript annotations from Gencode version M13.
Expression values were computed using RSEM version 1.2.28 and Gencode version M13 annotations (based on Ensembl 88).
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output (first line identifies the columns)

growth_protocol: All mice were bred and housed under specific-pathogen-free conditions in sterile ventilated racks at the Institute for Research in Immunology and Cancer. B.6SJL-Ptprca Pep3b/BoyJ-CD45.1 female mice (Jackson Laboratory, #002014, also called B6.SJL) were mated with BALB/cJ males (Jackson Laboratory, #000651). As lactation causes a delay in postpartum thymic regeneration, pups were removed at birth.

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA Hyperprep Stranded PolyA

treatment_protocol: Stromal cell enrichment was performed as described (16,17) Briefly, thymi were cut in small pieces in RPMI with HEPES (Gibco) at room temperature (r.t.), and gently agitated using P1000 pipet with wide-bore tips to remove thymocytes. This step was repeated until no more thymocytes were released (supernatant stayed translucid). Then, the supernatant was removed and replaced with 1 mL of RPMI with HEPES containing papain 0.5 mg/ml (Worthington Biochemical Corporation), DNase 0.1 mg/ml (Sigma) and collagenase IV 0.25 mg/ml (Sigma) and incubated at 37°C for 3 x 15 minutes. Stromal fragments were agitated using wide-bore tips first, and then standard P1000 tips between each incubation. After the second incubation, supernatant was removed and placed in a falcon tube containing 5 ml of PBS 1X with 0.5% bovine serum albumin (Sigma) at r.t. and the remaining stromal fragments were incubated once again with 1 ml of enzyme solution. Cells are pooled after the third incubation, centrifuged at 4°C and filtered. At this point, cells were kept at 4°C (or on ice) for antibody staining and analysis. Analysis of thymic epithelial populations were performed following enrichment of EpCAM+ cells using anti-EpCAM microbeads (mouse, Miltenyi) and LS or MS columns (Miltenyi Biotec), depending on the total number of cells after enzymatic digestion. Cells are directly sorted in Trizol and kept at -80C until RNA extraction.

tag: cell type

value: mTEC

value: NPC

tag: replicate


title: NPC-M1

description: age-matched non-pregnant female mice


title: 3068 Day 4 rep2 (dataset 2)

description: 3068 Day 4 rep2


title: h1_bisulfite_rep3


title: NL081

description: Patient 8


title: NPC-M3

description: age-matched non-pregnant female mice


title: NL101

description: Patient 10


title: h1_bisulfite_rep2


title: NPC-C5

description: age-matched non-pregnant female mice

source_name: cortical thymic epithelial cells

value: cTEC


title: 3068 Day 4 rep1 (dataset 2)

description: 3068 Day 4 rep1


title: NPC-C4

description: age-matched non-pregnant female mice


title: NL071

description: Patient 7

value: No Clinical Response


title: 3080 Day 7 Rep2

data_processing:
Sequenced reads were sorted wit samtools and deduplicated using Picard MarkDuplicates, then aligned to GCA_000223135.1 using HISAT2
Gene counts in exonic regions were calculated using featureCounts, then expressed in Reads Per Kilobase of exon per Megabase of library size (RPKM) with an R script
Genome_build: GCA_000223135.1
Supplementary_files_format_and_content: CSV text files include RPKM values for each sample


title: NPC-C1

description: age-matched non-pregnant female mice


title: wt_bisulfite_rep6


title: 3080 Day 7 Rep1


title: NL082

description: Patient 8


title: NL061

description: Patient 6


title: NL062

description: Patient 6


title: 3077 Day 7 Rep2


title: NL052

description: Patient 5


title: NL072

description: Patient 7


title: 3077 Day 7 Rep1


title: h1met1_RNA_leaves_rep9

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw

source_name: leaf tissue

extract_protocol:
1 mg of RNA was subjected to DNA-free DNA removal kit (Thermo, AM1907) to degrade DNA from samples. To remove rRNA, RNA was treated with RiboMinus Plant Kit for RNA-Seq (Invitrogen, A1083808).
To construct bisulfite sequencing libraries, about 500 ng of purified gDNA was fragmented to roughly 100-1000 bp then purified using 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was end-repaired and ligated to HPLC/PAGE purified, cytosine-methylated Illumina adapters (Elim Biopharmaceuticals, Inc.). DNA was subjected to two rounds of bisulfite conversion according to manufacturer's protocol (Qiagen, cat. No. 59104). To remove self-ligated adapters, DNA was purified twice with 0.8X volume of SPRI beads. NEB next indexing primers were used to amplify bisulfite-converted libraries (New England BIolabs Inc. cat. No. E7335S). DNA fragments isolated for ChIP-, ChAP-, and DnaseI-sequencing were subjected to Illumina library construction as described in bisulfite sequencing library construction except for the two rounds of bisulfite conversion.


title: h1met1_RNA_leaves_rep8

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: 3068 Day 7 Rep2


title: wt_bisulfite_rep5


title: h1_bisulfite_rep1


title: E18-M1


title: NL051

description: Patient 5


title: E18-C4


title: NL042

description: Patient 4


title: 3068 Day 7 Rep1


title: h1met1_RNA_leaves_rep6

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: h1met1_RNA_leaves_rep7

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: E18-M4


title: E18-C3


title: E18-C1


title: 3478 Day 7 Rep1


title: h1met1_RNA_leaves_rep5

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: NL032

description: Patient 3


title: NL031

description: Patient 3


title: h1met1_RNA_leaves_rep4

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: D8-M1


title: D8-C1


title: 3080 Day 4 Rep2


title: 3080 Day 4 Rep1


title: h1met1_RNA_leaves_rep2

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: NL011

description: Patient 1


title: NL041

description: Patient 4


title: NL012

description: Patient 1


title: h1met1_RNA_leaves_rep1

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: 3478 Day 7 Rep2


title: D6-M4


title: D6-M2


title: h1met1_RNA_leaves_rep3

description:
h1met1_leaf.f.bw
h1met1_leaf.r.bw


title: 37 °C control

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätsstraße 150

department: Microbial Biology

country: Germany

institute: Ruhr University Bochum

description: reads were sequenced on both Illumina HiSeq 2500 and Genome Analyzer IIx instruments.

data_processing:
adapter trimming using cutadapt
illumina read mapping to the Yersinia pseudotuberculosis transcriptome using bowtie version v0.12.8
counting of reverse transcription stop events per nucleotide using perl-script sam2tab.pl from Wan et al., 2013, Nature Protocolls
normalization between libraries using in-house python script
lead score calculation using in-house python script
Genome_build: NC_010465
Supplementary_files_format_and_content: tab-separated text file with a lead scores for each nucleotide of the Yersinia pseudotuberculosis transcriptome. The chromosomal TSS IDs are available at: http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/16-001//Annotation/cdRNA_chr.gff

organism: Yersinia pseudotuberculosis

source_name: bacterial culture

growth_protocol: Prior to treatment, cultures of Y. pseudotuberculosis YPIII were grown at 25 °C and 37 °C in LB medium  to an OD600 = 0.5

extract_protocol:
Total RNA was extracted using a hot phenol extraction protocol as described previously (Nuss et al., 2015, PLoS Genet)
rRNA depletion via RiboZero-Kit was followed by sonification to obtain a median fragment size of 200 nt. Afterwards, RNA 5'-ends were phosphorylated using T4 RNA ligase and adapters were ligated to the 5'- and 3'-end. cDNA was produced by reverse transcription, amplified via PCR (15 cycles) and purified via agarose gel (2% (w/v) agarose) electrophoresis (fragments 150-500 bp).

treatment_protocol: A 525 mM (final concentration 150 mM) and a 245 mM (final concentration 70 mM) lead acetate solution (4xLB + lead(II) acetate) was added to the culture grown at 25 °C and 37 °C, respectively. The cells were incubated under continuous shaking for 7 min, the reaction was stopped by addition of 10 ml cold 500 mM EDTA and cultures were placed on ice. Control sampleswere treated the same way as the lead treated samples except for the addition of 4x LB + distilled water instead of lead(II) acetate solution.

tag: strain

value: YPIII

tag: genotype


title: 3077 Day 4 Rep1

source_name: CHO suspension culture

tag: cell line

tag: day


title: 37 °C + lead(II) acetate


title: met1_RNA_leaves_rep6

description:
met1_leaf.f.bw
met1_leaf.r.bw

tag: genotype/variation


title: NL142

description: Patient 14


title: 3068 Day 4 Rep2


title: D6-M1


title: met1_RNA_leaves_rep5

description:
met1_leaf.f.bw
met1_leaf.r.bw


title: 25 °C + lead(II) acetate


title: D6-C5


title: 25 °C control


title: 3068 Day 4 Rep1


title: met1_RNA_leaves_rep4

description:
met1_leaf.f.bw
met1_leaf.r.bw


title: D6-C4


title: Restrictive_W23_2_0mm_2_RNAseq

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: RNA library from Maize WT (W23), 2.0 mm anthers. Plants were germinated and growing at 28 C/22 C in the day/night until samples were collected. Sample was collected by Chong Teng in the Meyers lab. The RNA library was constructed by Chong Teng with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Library was submitted by Chong Teng for sequencing at DBI in the University of Delaware.

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 50 nucleotides. RNA-seq reads were mapped to the maize genome (Maize Genome Database).
Genome_build: version 4 of the B73 maize genome
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences
Supplementary_files_format_and_content: Text containing distinct RNA-seq reads with their raw abundance after removing the adapter sequences

organism: Zea mays

source_name: Whole anther

extract_protocol: Small RNA libraries and RNA-seq libraries were constructed from total RNA isolated from anthers of Zea mays using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on the preparation guide of RealSeq®-AC kits (SomaGenics). And the RNA-seq library preparation protocol is based on NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs®) Preparation Guide. The libraries were sequenced on an Illumina NextSeq at the Delaware Biotechnology Institute (Newark, DE). "

value: WT, W23 inbred

value: Whole anther

tag: anther length

tag: growth temperature

value: growing at 28 C/22 C in the day/night


title: E18-M3

tag: timepoint


title: met1_RNA_leaves_rep3

description:
met1_leaf.f.bw
met1_leaf.r.bw


title: Restrictive_W23_2_0mm_1_RNAseq


title: D6-C2


title: 3478 Day 4 Rep1


title: met1_RNA_leaves_rep2

description:
met1_leaf.f.bw
met1_leaf.r.bw


title: D5-M1


title: 3077 Day 4 Rep2


title: met1_RNA_leaves_rep1

description:
met1_leaf.f.bw
met1_leaf.r.bw


title: D5-C1


title: Permissive_W23_2_0mm_2_RNAseq

description: RNA library from Maize WT (W23), 2.0 mm anthers. Plants were germinated and growing at 28 C/22 C in the day/night for 3 weeks then shifted to 22 C/20 C greenhouse until samples were collected. Sample was collected by Chong Teng in the Meyers lab. The RNA library was constructed by Chong Teng with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Library was submitted by Chong Teng for sequencing at DBI in the University of Delaware.


title: Permissive_W23_2_0mm_1_RNAseq

value: growing at 28 C/22 C in the day/night for 3 weeks then shifted to 22 C/20 C greenhouse


title: D4-M1


title: NL111

description: Patient 11


title: h1_RNA_rep3

description:
h1_seedling.f.bw
h1_seedling.r.bw


title: Restrictive_W23_2_0mm_2_sRNAseq

description: sRNA library from Maize WT (W23) 2.0 mm anthers, growing under restrictive temperature (28 C/22 C). Sample was collected by Chong Teng in the Meyers lab. The sRNA library was constructed by Chong Teng with RealSeq-AC kit (Somagenics). Library was submitted by Chong Teng for sequencing at DBI in the University of Delaware.

value: restrictive temperature (28 C/22 C)


title: h1_RNA_rep2

description:
h1_seedling.f.bw
h1_seedling.r.bw


title: D4-C1


title: Restrictive_W23_2_0mm_1_sRNAseq


title: h1_RNA_rep1

description:
h1_seedling.f.bw
h1_seedling.r.bw


title: wBm Agilent SureSelect, vector, 4 dpi, a, SRX2508250

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

description:
wbm_counts.txt
wbm_tpm.txt

data_processing:
Reads aligned to a combined A. aegypti, B. malayi, and wBm reference using TopHat v1.4 (for poly(A) selection and B. malayi Agilent SureSelect samples) or Bowtie v0.12.9 (for poly(A) depletion and wBm Agilent SureSelect samples)
Protein-coding genes for B. malayi and A. aegypti quantified using HTSeq v0.5.3p9 with mode set to union. Protein-coding genes for wBm quantified using FADU v1.2.
Differentially expressed genes for all three organisms were individually identified using edgeR v3.20.1
TPM values calculated for protein-coding genes
Expression modules for differentially expressed genes for all three organisms identified using WGCNA v1.61
Significantly over-represented functional terms identified using Fisher's exact test for each WGCNA module
Genome_build: Brugia malayi WS259, Wolbachia endosymbiont strain TRS of Brugia malayi (NC_006833.1), and Aedes aegypti AaegL3.3
Supplementary_files_format_and_content: tab-delimited files containing counts, TPM, WGCNA module assignments for differentially expressed genes, functional term enrichment analyses for WGCNA modules for both B. malayi and A. aegypti

organism:
Brugia malayi
Aedes aegypti
Wolbachia endosymbiont of Brugia malayi

source_name: B. malayi taken from A. aegypti 4 dpi

extract_protocol:
For nematode samples, third stage larvae of Brugia malayi strain FR3 were isolated from infected mosquitoes 9-16 days post infection (dpi) using the NIAID/NIH Filariasis Research Reagent Resource Center (FR3) Research Protocol 8.4. Larvae were isolated in RPMI + P/S, enumerated, and either flash frozen in liquid nitrogen for storage at -80°C or used for the infection of male Mongolian gerbils (Meriones unguiculatus; Charles River, Wilmington, MA, USA). Gerbils were anesthetized with 5% isoflurane and infected by introducing 400 L3s into the peritoneal cavity using a butterfly catheter. Larvae, immature adults, and mature adults were recovered by peritoneal flush using a terminal procedure. Brugia malayi embryos were collected from live gravid females as previously described. For vector samples, the Aedes aegypti black-eyed Liverpool strain was obtained from FR3 and maintained in the Biosafety Level 2 Insectary at the University of Wisconsin Oshkosh. Desiccated mosquito eggs were hatched in deoxygenated water and the resulting larvae were maintained on a slurry of ground TetraMin fish food (Blacksburg, VA) at 27°C with 80% relative humidity. Female pupae were separated using a commercial larva pupa separator (The John Hock Company, Gainesville, FL), placed in mesh-covered paper soup cartons, and enclosed adults were fed with cotton pads soaked in sucrose solution. Females were deprived of sucrose approximately twelve hours prior to blood feeding. Mosquitoes were infected with the Brugia malayi FR3 strain by feeding microfilaremic cat blood (FR3) through Parafilm via a glass-jacketed artificial membrane feeder. When necessary microfilaremic cat blood was diluted with uninfected dog blood to achieve a suitable parasite density for infection (100-250 microfilariae/20 μL). Infected mosquitoes were collected at 18 hours post infection (hpi), 4 dpi, and 8 dpi. They were anesthetized with CO2 then transferred to chilled microscope slides where the legs, wings, heads and abdomens were removed. The thoraces with and without developing B. malayi larvae were flash frozen in liquid nitrogen and stored at -80 °C prior to RNA isolation. Vector-derived Infective B. malayi L3 were isolated from whole mosquitoes in bulk using the standard FR3 protocol. For RNA isolation, mosquito thoraces were combined with TRIzol (Zymo Research, Irvine, CA) at a ratio of 1 mL TRIzol per 50-100 mg mosquito tissue, while nematode samples were processed using a 3:1 volume ratio of TRIzol to sample. For both preparations, 1 µL β-mercaptoethanol was added for every 100 µL of sample. The tissues were homogenized using a bead beater and a TissueLyser (Qiagen, Germantown, MD) at 50 Hz for 5 min. The homogenate was then transferred to a new tube and centrifuged at 12,000g for 10 min at 4°C. After incubation at room temperature for 5 min, 0.2 mL chloroform was added for every 1 mL TRIzol. The samples were shaken by hand for 15 s, incubated at room temperature for 3 min, loaded into a pre-spun Phase Lock Gel heavy tube (5Prime, Gaithersburg, MD), and centrifuged at 12,000g for 5 min at 4°C. The upper phase was extracted, one volume of 100% ethanol was added, and then loaded onto a PureLink RNA Mini column (Ambion, Austin, TX). The samples were processed following manufacturer instructions, quantified using a Qubit fluorometer (Qiagen, Germantown, MD) and Nanodrop spectrometer (Nanodrop, Wilmington, DE), and sent to Institute for Genomic Sciences at the University of Maryland Baltimore for DNase treatment and library preparation.
Whole transcriptome libraries without AgSS capture were constructed for sequencing on the Illumina platform using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA). For targeting eukaryotic mRNA, polyadenylated RNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module. For the B. malayi and wBm AgSS capture designs, probes were designed using the SureSelect DNA Advanced Design Wizard for B. malayi and wBm. When targeting bacterial mRNA, samples underwent rRNA- and poly(A)-reductions. Probes were designed to capture every 120 bp for each coding sequence in both organisms with no overlap between baits. DustMasker was used to identify and mask low complexity regions of the genome from the probe design .For samples treated with the wBm AgSS capture, pre-capture libraries were constructed from 500-1000 ng of total RNA samples using the NEBNext Ultra Directional RNA Library Prep kit (NEB, Ipswich, MA, USA). First strand cDNA was synthesized without mRNA extraction to retain non-polyadenylated transcripts and fragmented at 94 oC for 8 min. After adaptor ligation, cDNA fragments were amplified with 10 cycles of PCR before capture. Wolbachia transcripts were captured from 200 ng of the amplified libraries using the Agilent SureSelectXT RNA (0.5-2 Mbp) bait library designed specifically for wBm. Library-bait hybridization reactions were incubated at 65 °C for 24 h then bound to MyOne Streptavidin T1 dynabeads (Invitrogen, Carlsbad, CA, USA). After multiple washes, bead-bound captured library fragments were amplified with 18 cycles of PCR. The libraries were loaded on an Illumina HiSeq4000, generating 151-bp paired end reads. For samples treated with the B. malayi AgSS capture, pre-capture libraries were constructed from 1000 ng of total RNA samples using the NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420, Ipswich, MA, USA). After adaptor ligation, cDNA fragments were amplified for 10 cycles of PCR before capture. B. malayi transcripts were captured from 200 ng of the amplified libraries using an Agilent SureSelectXT Custom (12-24 Mbp) bait library designed specifically for B. malayi. Library-bait hybridization reactions were incubated at 65 °C for 24 h then bound to MyOne Streptavidin T1 Dynabeads (Invitrogen, Carlsbad, CA). After multiple rounds of washes, bead-bound captured library fragments were amplified with 16 cycles of PCR. The libraries were loaded on a Illumina HiSeq 4000 generating 151-bp paired end reads.

tag: brugia malayi strain

tag: aedes aegypti strain

value: black-eyed Liverpool

tag: enrichment method

value: wBm Agilent SureSelect capture


title: wBm Agilent SureSelect, vector, 8 dpi, a, SRX2508253

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi taken from A. aegypti 8 dpi


title: wBm Agilent SureSelect, vector, 8 dpi, b, SRX2508254

description:
wbm_counts.txt
wbm_tpm.txt


title: wBm Agilent SureSelect, vector, 4 dpi, b, SRX2508251, SRX2508252

description:
wbm_counts.txt
wbm_tpm.txt


title: Permissive_W23_2_0mm_2_sRNAseq

description: sRNA library from Maize WT (W23) 2.0 mm anthers, growing under permissive temperature (22 C/20 C). Sample was collected by Chong Teng in the Meyers lab. The sRNA library was constructed by Chong Teng with RealSeq-AC kit (Somagenics). Library was submitted by Chong Teng for sequencing at DBI in the University of Delaware.

value: permissive temperature (22 C/20 C)


title: D3-M3

source_name: medullary thymic epithelial cells


title: 3478 Day 4 Rep2


title: wBm Agilent SureSelect, vector, 18 hpi, b, SRX2508249

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi taken from A. aegypti 18 hpi


title: wt_RNA_rep7

description:
col_h1ctrl_seedling_f.bw
col_h1ctrl_seedling_r.bw

value: wild type


title: D3-M2


title: Permissive_W23_2_0mm_1_sRNAseq


title: wBm Agilent SureSelect, vector, 18 hpi, a, SRX2508248

description:
wbm_counts.txt
wbm_tpm.txt


title: dcl5mu03_2_0mm_sRNA

description: sRNA library from Maize dcl5-mu03 (mu-illumina_139042.7 Ear: V610-3) 1.5 - 2.0 mm anthers, fertile. Sample was collected by Chong Teng in the Meyers lab. The sRNA library was constructed by Chong Teng with RealSeq-AC kit (Somagenics). Library was submitted by Chong Teng for sequencing at DBI in the University of Delaware.

value: Mutant, dcl5-mu03


title: wt_RNA_rep6


title: wt_RNA_rep5


title: B.malayi Agilent SureSelect, vector, 8 dpi, a, SRX2505955

description:
bmalayi_counts.txt
bmalayi_tpm.txt

tag: developmental stage

value: vector, 8 dpi

value: B. malayi Agilent SureSelect capture


title: D3-C3


title: wt_RNA_leaves_rep9

description:
col_leaf.f.bw
col_leaf.r.bw


title: NDNs isolated from patient 8

city: Pieve Emanuele

first: Elvezia

middle: Maria

last: Paraboschi

address: via Rita Levi Montalcini 4

department: Department of Biomedical Sciences

country: Italy

institute: Humanitas University

description: PATIENT 8_NDN

data_processing:
Data were analysed using the RT² Profiler PCR Array Qiagen data analysis software, and ACTB and B2M as housekeeping genes
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control changes

label: SYBR Green

source_name: normal-density neutrophils

label_protocol: RT-PCR assays were performed using the RT2 Profiler PCR Array Human Innate & Adaptive Immune Responses array (Qiagen), and  a real-time PCR detection system (QuantStudio 7 Flex Real-Time PCR System, Thermo Fisher Scientific) with a two-step thermal cycling: 95 °C for 10 min, followed by 40 cycles (95 °C for 15 sec, 60 °C for 1 min). Total RNA (600 ng) was reverse transcribed using the RT2 First Strand Kit (SABiosciences, Qiagen, UK).

extract_protocol: Total RNA was extracted with Maxwell® RSC miRNA Tissue kit

tag: subject status

value: patients affected by tubercolosis (TB)

value: neutrophils

tag: cell subtype

value: normal-density neutrophils

tag: sample group

value: control


title: wt_RNA_leaves_rep8

description:
col_leaf.f.bw
col_leaf.r.bw


title: B.malayi Agilent SureSelect, vector, 8 dpi, b, SRX2505953

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: D3-C2

tag: cell type

value: cTEC


title: B.malayi Agilent SureSelect, vector, 4 dpi, b, SRX2505771

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: vector, 4 dpi


title: D3-C1

tag: replicate


title: LDNs isolated from patient 8

description: PATIENT 8_LDN

source_name: low-density neutrophils

value: low-density neutrophils

value: test


title: wt_RNA_leaves_rep7

description:
col_leaf.f.bw
col_leaf.r.bw


title: B.malayi Agilent SureSelect, vector, 4 dpi, a, SRX2505770

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: wt_RNA_leaves_rep6

description:
col_leaf.f.bw
col_leaf.r.bw


title: D2-C1


title: B.malayi Agilent SureSelect, vector, 18 hpi, b, SRX2505769

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: vector, 18 hpi


title: wt_RNA_leaves_rep5

description:
col_leaf.f.bw
col_leaf.r.bw


title: D3-M1

value: mTEC


title: D28-M1


title: wt_RNA_leaves_rep4

description:
col_leaf.f.bw
col_leaf.r.bw


title: LDNs isolated from patient 7

description: PATIENT 7_LDN


title: 3068 Seed train rep2 (dataset 2)

description: 3068 Seed train rep2


title: NDNs isolated from patient 7

description: PATIENT 7_NDN


title: NDNs isolated from patient 6

description: PATIENT 6_NDN


title: AgNO3-3

city: beijing

first: liu

last: xintong

institute: China Agricuture university

description:
TRANSCRIPTOMIC
AgNO3_FPKM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rosa chinensis（Oldblash） whole genome using tophat2.1.1with 2 mismatches allowed
Cuffquant 2.2.0 to construct transcripts of each sample separately，and Cuffdiff to get DEG

organism: Rosa hybrid cultivar

source_name: samantha

growth_protocol: 'Samantha' were grown in were grown under a plastic cover in Changping District (40°139N, 116°129E), Beijing, China. In Spring of 2018, cut flower samples were harvested at developmental stage 2 of flower opening

extract_protocol:
rose petal flash frozen on dry ice, and RNA was harvested using hot borate reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
De novo Liberary

treatment_protocol: ose flower under treatment of various plant hormones, including ethylene, 2,4-D, NAA, cytok, gibberellins, abscisic acid, brassinosteroids, salicylic acid, jasmonates, as well as ethylene inhibitor 1-MCP and AgNO.

value: Level 2

tag: tissue

value: petal

tag: layer number

value: outer


title: D28-C1


title: AgNO3-2

description:
TRANSCRIPTOMIC
AgNO3_FPKM.txt


title: wt_RNA_leaves_rep3

description:
col_leaf.f.bw
col_leaf.r.bw

value: wild type


title: LDNs isolated from patient 6

description: PATIENT 6_LDN


title: D24-C1


title: wt_RNA_leaves_rep2

description:
col_leaf.f.bw
col_leaf.r.bw


title: AgNO3-1

description:
TRANSCRIPTOMIC
AgNO3_FPKM.txt


title: D2-M1


title: 1-MCP-3

description:
TRANSCRIPTOMIC
1-MCP_FPKM.txt


title: wt_RNA_leaves_rep1

description:
col_leaf.f.bw
col_leaf.r.bw


title: single_myofiber_from_young_mouse_F1_2

tag: strain

tag: age

value: young (4 weeks)

value: Extensor digitorum longus myofibers


title: D20-M1


title: NDNs isolated from patient 4

description: PATIENT 4_NDN


title: B.malayi Agilent SureSelect, vector, 18 hpi, a, SRX2505171

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: black-eyed Liverpool

value: B. malayi Agilent SureSelect capture


title: wt_decap_rep5

description:
decap_col.f.bw
decap_col.r.bw

extract_protocol:
10 mg of RNA was subjected to DNA-free DNA removal kit (Thermo, AM1907) to degrade DNA from samples. To remove rRNA, RNA was treated with RiboMinus Plant Kit for RNA-Seq (Invitrogen, A1083808). rRNA-depleted total RNA was chemically fragmented, then dephhorylated using Antarctic phosphatase (NEB, M0289).  5' cap of RNA was removed by incubating with RNA 5' pyrophosphohydrolase (RppH, NEB M0356) in 1X Thermopol buffer (NEB B9004S). DECAP-seq libraries were constructed using TruSeq small RNA library prep kit (Illumina, RS-200-0012). To prevent 21- or 24-nt sRNA contamination, library fragments larger than 180 bp were selected for sequencing.
To construct bisulfite sequencing libraries, about 500 ng of purified gDNA was fragmented to roughly 100-1000 bp then purified using 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was end-repaired and ligated to HPLC/PAGE purified, cytosine-methylated Illumina adapters (Elim Biopharmaceuticals, Inc.). DNA was subjected to two rounds of bisulfite conversion according to manufacturer's protocol (Qiagen, cat. No. 59104). To remove self-ligated adapters, DNA was purified twice with 0.8X volume of SPRI beads. NEB next indexing primers were used to amplify bisulfite-converted libraries (New England BIolabs Inc. cat. No. E7335S). DNA fragments isolated for ChIP-, ChAP-, and DnaseI-sequencing were subjected to Illumina library construction as described in bisulfite sequencing library construction except for the two rounds of bisulfite conversion.

tag: genotype/variation


title: LDNs isolated from patient 5

description: PATIENT 5_LDN

value: patients affected by tubercolosis (TB)

value: neutrophils


title: 1-MCP-2

description:
TRANSCRIPTOMIC
1-MCP_FPKM.txt


title: LDNs isolated from patient 4

description: PATIENT 4_LDN


title: 1-MCP-1

description:
TRANSCRIPTOMIC
1-MCP_FPKM.txt


title: D20-C1


title: NDNs isolated from patient 5

description: PATIENT 5_NDN

value: normal-density neutrophils

value: control


title: D1-M1


title: D1-C1

value: cTEC


title: D24-M1


title: D16-M1


title: NDNs isolated from patient 2

description: PATIENT 2_NDN


title: LDNs isolated from patient 3

description: PATIENT 3_LDN

value: low-density neutrophils


title: ET-1

description:
TRANSCRIPTOMIC
ET_FPKM.txt


title: Ntert si-iASPP

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Samples were hybridized to oligonucleotide glass arrays with sequences representing probes for human microRNAs from the Sanger database v19 (Human miRNA 8x60K Microarray Version 19, Agilent Technologies).

scan_protocol: After 20 hours, slides were washed and scanned using an Agilent C dual-laser microarray scanner. Images obtained were analysed using Feature Extraction software v10.5.

data_processing: Raw data extracted from each image was processed using R statistical environment and the linear modelling for microarray analysis library. A filtering function was applied to select only ‘well above background’ features. Cy3 median signal was log transformed and background subtracted using the ‘normexp’ method, with an offset of 20. Between-array normalisation was applied, using the ‘quantile’ method and signals from replicated probes were averaged.

source_name: Immortalized normal keratinocyte cell line

label_protocol: MiRNA expression profiling was carried out using the one-colour labelling method. Labelling, hybridization, washing and slide scanning were performed following manufacturers’ protocols (Agilent Technologies). Briefly, 100ng of total RNA were dephosphorylated and denatured; then a ligation and labeling step with Cy3 was performed.

growth_protocol: Cutaneous SCC cell lines were generated by the Cancer Research UK Skin Tumour Laboratory. Together with the N-TERT cell line, they were maintained in DMEM:F12 media at a 3:1 ratio supplemented with 10% FCS, 2mM L-glutamine, 5,000U/ml Penicillin, 5,000μg/ml Streptomycin. An additional keratinocyte supplement was added to the media containing 5μg/ml Transferrin, 0.4μg/ml hydrocortisone, 10-10M cholera toxin, 5μg/ml insulin, 2x10-11M liothyronine and 10ng/ml EGF. During differentiation assays cells were maintained in EpiLife® Medium, (60μM calcium) supplemented with Human Keratinocyte Growth Supplement (Life Technologies).

extract_protocol: Total RNA were extracted using the miRNeasy Mini Kit (Qiagen, UK) according to the manufacturer’s instructions. The RNA concentration for each sample was measured using a Nanodrop ND-1000 spectrophotometer at an absorbance of 260nm.

treatment_protocol: Cells were silenced using transfection reagent DharmaFECT 1® (Thermo Scientific) according to the manufacturer’s instructions.

tag: sirna

value: iASPP


title: ET-2

description:
TRANSCRIPTOMIC
ET_FPKM.txt


title: Ntert scramble

value: Immortalized normal keratinocyte cell line

value: scramble


title: LDNs isolated from patient 2

description: PATIENT 2_LDN

value: test


title: AIR-2

description:
TRANSCRIPTOMIC
AIR_FPKM.txt

value: Level 2

value: petal


title: AIR-3

description:
TRANSCRIPTOMIC
AIR_FPKM.txt

value: outer


title: D16-C1


title: IC4 si-iASPP

source_name: Cutaneous squamous cell carcinoma

value: Cutaneous squamous cell carcinoma cell line


title: NDNs isolated from patient 3

description: PATIENT 3_NDN


title: IC18 scramble


title: poly(A)-selection, jird, mature microfilariae, a, SRX2416292, SRX2416293

description:
bmalayi_counts.txt
bmalayi_tpm.txt

organism:
Brugia malayi
Wolbachia endosymbiont of Brugia malayi

source_name: B. malayi mature microfilariae taken from jirds

value: jird, mature microfilariae

value: poly(A)-enrichment


title: D12-M3

value: mTEC


title: D12-M2


title: AIR-1

description:
TRANSCRIPTOMIC
AIR_FPKM.txt


title: LOUCY DMSO_anti-Pol II (S5P)_ChIP

city: Ibaraki

first: Masahiro

last: Oka

state: Osaka

address: 7-6-8 Saito-Asagi

country: Japan

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

data_processing:
Reads were mapped to the humane (resp. mouse) reference genome GRCh38 (resp. GRCm38) using the HISAT software (v2.1.0).
Only unireads were retained and duplicates were removed.
The resulting BAM files were input to the deepTools (v.3.1.3) suite to generate bigWig files in 100bp bins smoothed over 100bp windows with RPKM normalization.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: bigWig files were generated for ChIP-seq signal visualization.

source_name: LOUCY

extract_protocol:
The cross-linked chromatin was sheared by sonication, and MNase treatment.
To repair ChIP-DNA and Input-DNA ends, T4 DNA polymerase, Klenow enzyme and T4 polynucleotide kinase were used (New England Biolabs), and an A base was subsequently added to the 3'-end by the treatment of Klenow exo-. The adaptor ligation and the PCR amplification for 18 cycles of DNA fragments were performed with Illumina (PCR primer InPE1.0 & InPE2.0).

value: human leukemia

tag: cell line

value: LOUCY

tag: chip antibody

value: anti-RNA Pol II (S5P) (clone 1H4B6), BMC Genomics. 2011;12:516


title: LOUCY KPT-330_anti-Pol II (S5P)_ChIP


title: LDNs isolated from patient 1

description: PATIENT 1_LDN

value: patients affected by tubercolosis (TB)

value: neutrophils


title: D12-M1

tag: timepoint


title: poly(A)-depletion, jird, 1 dpi, b, SRX2416089, SRX2416090

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi taken from jirds 1 dpi

tag: brugia malayi strain

value: rRNA-, poly(A)-depletion


title: LOUCY KPT-330_anti-Pol II (S2P)_ChIP

value: anti-RNA Pol II (S2P) (clone 3E7C7), BMC Genomics. 2011;12:516


title: ET-3

description:
TRANSCRIPTOMIC
ET_FPKM.txt


title: D12-C3

source_name: cortical thymic epithelial cells

value: cTEC


title: IC18 si-iASPP

value: iASPP


title: IC4 scramble

value: scramble


title: SA-2

description:
TRANSCRIPTOMIC
SA_FPKM.txt

value: Level 2


title: poly(A)-depletion, jird, 2 dpi, b, SRX2416087, SRX2416088

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi taken from jirds 2 dpi

tag: enrichment method


title: LOUCY DMSO_anti-Pol II (S2P)_ChIP


title: poly(A)-depletion, jird, mature microfilariae, a, SRX2416085, SRX2416086

description:
wbm_counts.txt
wbm_tpm.txt


title: D12-C2


title: LOUCY KPT-330_INPUT both anti-RNA Pol II ChIPs

description: INPUT for both anti-RNA Pol II (S2P) and (S5P) ChIP

value: INPUT


title: D12-C1


title: NDNs isolated from patient 1

description: PATIENT 1_NDN

value: normal-density neutrophils

value: control


title: LOUCY DMSO_INPUT both anti-RNA Pol II ChIPs


title: JA-3

description:
TRANSCRIPTOMIC
JA_FPKM.txt

tag: developmental stage

value: petal

value: outer


title: D10-M1

value: mTEC


title: poly(A)-depletion, jird, immature microfilariae, a, SRX2416083, SRX2416084

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi immature microfilariae taken from jirds


title: poly(A)-depletion, jird, 2 dpi, a, SRX2416009, SRX2416010

description:
wbm_counts.txt
wbm_tpm.txt


title: JA-2

description:
TRANSCRIPTOMIC
JA_FPKM.txt


title: OCI-AML3_anti-NPM1c_ChIP

value: human leukemia


title: JA-1

description:
TRANSCRIPTOMIC
JA_FPKM.txt


title: D10-C1


title: OCI-AML3_INPUT

description: INPUT for anti-NPM1(mutant)(ThermoFischer, PA1-46356) ChIP


title: SA-3

description:
TRANSCRIPTOMIC
SA_FPKM.txt


title: poly(A)-selection, jird, 1 dpi, b, SRX2415910, SRX2415911

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: jird, 1 dpi

value: poly(A)-enrichment


title: poly(A)-depletion, jird, 1 dpi, a, SRX2415978, SRX2415979

description:
wbm_counts.txt
wbm_tpm.txt


title: LOUCY KPT-330_anti-Nup214_ChIP

value: LOUCY


title: poly(A)-selection, jird, 2 dpi, b, SRX2415908, SRX2415909

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: jird, 2 dpi


title: GA-2

description:
TRANSCRIPTOMIC
GA_FPKM.txt


title: LOUCY DMSO_anti-Nup214_ChIP


title: D0-M2


title: poly(A)-selection, jird, immature microfilariae, a, SRX2415043, SRX2415044

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: jird, immature microfilariae


title: SA-1

description:
TRANSCRIPTOMIC
SA_FPKM.txt


title: GA-1

description:
TRANSCRIPTOMIC
GA_FPKM.txt


title: LOUCY KPT-330_INPUT for anti-Nup214_ChIP

description: INPUT for anti-Nup214(Bethyl Laboratories, A300-716A) ChIP


title: D0-C4


title: ABA-3

description:
TRANSCRIPTOMIC
ABA_FPKM.txt


title: poly(A)-selection, jird, 2 dpi, a, SRX2414981, SRX2414982

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: LOUCY DMSO_INPUT for anti-Nup214_ChIP


title: D0-C2


title: poly(A)-selection, jird, 1 dpi, a, SRX2409229, SRX2409230

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: LOUCY_anti-Crm1_ChIP

value: anti-Crm1 (Bethyl Laboratories, A300-469A)


title: D0-C1

value: cTEC


title: LOUCY_INPUT

description: INPUT for anti-Crm1 (Bethyl Laboratories, A300-469A) ChIP


title: ABA-1

description:
TRANSCRIPTOMIC
ABA_FPKM.txt


title: 6-BA-3

description:
TRANSCRIPTOMIC
6-BA_FPKM.txt


title: HL60_DMSO_anti-Crm1_ChIP

value: anti-Crm1 (CST, 46249)


title: poly(A)-selection, jird, 24 dpi immature female, b, SRX1539871

description:
bmalayi_counts.txt
bmalayi_tpm.txt

source_name: B. malayi immature females taken from jirds 24 dpi

value: jird, 24 dpi immature female


title: poly(A)-selection, jird, mature microfilariae, b, SRX1539874, SRX1539875

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: jird, mature microfilariae


title: GA-3

description:
TRANSCRIPTOMIC
GA_FPKM.txt

value: Level 2


title: poly(A)-selection, jird, immature microfilariae, b, SRX1539873

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: LOUCY_KPT-330_anti-Crm1_ChIP


title: 6-BA-2

description:
TRANSCRIPTOMIC
6-BA_FPKM.txt


title: D0-M1


title: 6-BA-1

description:
TRANSCRIPTOMIC
6-BA_FPKM.txt


title: poly(A)-selection, jird, 24 dpi immature female, a, SRX1539869

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: LOUCY_DMSO_anti-Crm1_ChIP


title: B1_B_Data1

city: Qingdao

first: Dan

last: Zhang

address: Yushan Road 5

department: Fisheries College

institute: Ocean University of China

data_processing:
Differential gene expression analysis was performed using ANOVO analysis for comparisons among samples with two biological replicates. For all comparisons, read counts were normalized to the aligned RPKM to obtain the relative levels of expression. The fold change cut-off was set at two fold with p-value < 0.05.
Genome_build: denovo sequencing
Supplementary_files_format_and_content: gene annotation (txt);transcript expression (txt);differential expression (txt)

organism: Penaeus vannamei

source_name: gill, brackish water cultured

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) with RIN number > 7.0.
Gills from L. vannamei were collected and samples were stored in RNAlater, and Total RNA was extracted using Trizol reagent. mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA) was used with 5 ug of total RNA for the construction of sequencing libraries.

value: juvenile

value: gill

tag: treatment

value: brackish water cultured


title: poly(A)-selection, jird, 20 dpi immature male, b, SRX1539865

description:
bmalayi_counts.txt
bmalayi_tpm.txt

source_name: B. malayi immature males taken from jirds 20 dpi

value: jird, 20 dpi immature male


title: B2_B_Data1


title: F1_F_Data1

source_name: gill, fresh water cultured

value: fresh water cultured


title: OCI-AML3_DMSO_anti-Crm1_ChIP

value: human leukemia


title: S2_S_Data1

source_name: gill, seawater cultured

value: seawater cultured


title: ABA-2

description:
TRANSCRIPTOMIC
ABA_FPKM.txt

value: petal

value: outer


title: poly(A)-selection, jird, 20 dpi immature male, a, SRX1539862

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: poly(A)-enrichment


title: F2_F_Data1


title: K562_DMSO_anti-Crm1_ChIP


title: poly(A)-selection, jird, 8 dpi, b, SRX1539819

description:
bmalayi_counts.txt
bmalayi_tpm.txt

source_name: B. malayi taken from jirds 8 dpi

value: jird, 8 dpi


title: S1_S_Data1


title: HL60_DMSO_INPUT

description: INPUT for anti-Crm1 (CST, 46249) ChIP

value: INPUT


title: poly(A)-selection, jird, 8 dpi, a, SRX1539817

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: D0-M4

source_name: medullary thymic epithelial cells

value: mTEC


title: BR-1

description:
TRANSCRIPTOMIC
BR_FPKM.txt


title: 21dpab_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11) using STAR 2.6.0c with the parameter “--outFilterMismatchNoverLmax 0.1 --alignIntronMax 200000” (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 12.04.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: danrer11 / GRCz11
Supplementary_files_format_and_content: The tab-delimited matrix with DESeq normalized counts.

organism: Danio rerio

source_name: 2 hearts

extract_protocol:
For RNA-seq, RNA was isolated from the laser microdissected samples using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip GxTouch 24 (Perkin Elmer).
20 ng of total RNA was used as input for PolyA enrichment (NEXTflexTM PolyA Beads) followed by library preparation using NEXTflexTM Rapid Directional qRNA-SeqTM Kit (Bioo Scientific Corp). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in average of 38M reads per library with 2x75bp paired end setup.

treatment_protocol: Valve cell ablation was performed by treating the fish with 2.5 mM Metronidazole for 6 hours. Fish were treated in individual containers and were kept in the dark during treatments.

tag: time after injury

value: 21 days


title: poly(A)-selection, jird, 4 dpi, b, SRX1539813

description:
bmalayi_counts.txt
bmalayi_tpm.txt

source_name: B. malayi taken from jirds 4 dpi

value: jird, 4 dpi


title: LOUCY_KPT-330_INPUT

description: INPUT for anti-Crm1 (CST, 46249) ChIP

value: LOUCY


title: 2,4D-3

description:
TRANSCRIPTOMIC
2,4-D_FPKM.txt

source_name: samantha

value: Level 2


title: 21dpab_2


title: LOUCY_DMSO_INPUT

description: INPUT for anti-Crm1 (CST, 46249) ChIP


title: 21dpab_1


title: BR-3

description:
TRANSCRIPTOMIC
BR_FPKM.txt


title: 2,4D-2

description:
TRANSCRIPTOMIC
2,4-D_FPKM.txt


title: poly(A)-selection, jird, 4 dpi, a, SRX1539799

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: 2,4D-1

description:
TRANSCRIPTOMIC
2,4-D_FPKM.txt


title: K562_DMSO_INPUT

description: INPUT for anti-Crm1 (CST, 46249) ChIP


title: OCI-AML3_DMSO_INPUT

description: INPUT for anti-Crm1 (CST, 46249) ChIP


title: 48hpab_3

value: 48 hours


title: poly(A)-depletion, jird, immature microfilariae, b, SRX1539795

description:
wbm_counts.txt
wbm_tpm.txt

value: rRNA-, poly(A)-depletion


title: IELKO16_2

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: library of 96 TBGR C-mycD/DCd4 IELP cells

growth_protocol: Mice were housed under SPF condition at the department of medical microbiology and hygiene of the university medical center Freiburg in accordance with the local animal care committiees and Regierungspräsidium Freiburg

extract_protocol:
IELPs were isolated by dissecting the thymus and single cell suspension of the thymus was isolated by mashing the tissue through a 70µm cell strainer with 15ml PBS. Lymphocytes were enriched by performing red cell lysis and IELPs were enriched by depleting CD4+ and CD8+ thymocytes by incubation with anti-CD4 and anti-CD8 purified antibodies and anti-mouse Dynabeads.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

tag: strain background

value: TBGR

value: 2 wk

value: Thymus

value: intraepithelial lymphocytes (IELs)


title: poly(A)-depletion, jird, 24 dpi immature female, b, SRX1539759

description:
wbm_counts.txt
wbm_tpm.txt


title: poly(A)-depletion, jird, mature microfilariae, b, SRX1539797, SRX1539798

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi mature microfilariae taken from jirds


title: NAA-1

description:
TRANSCRIPTOMIC
NAA_FPKM.txt


title: NAA-2

description:
TRANSCRIPTOMIC
NAA_FPKM.txt


title: BR-2

description:
TRANSCRIPTOMIC
BR_FPKM.txt


title: IELKO16_1

tag: cell type


title: H2O-3

description:
TRANSCRIPTOMIC
H2O_FPKM.txt


title: uninjured_3

value: uninjured


title: IELKO15_2


title: poly(A)-depletion, jird, 24 dpi immature female, a, SRX1539757

description:
wbm_counts.txt
wbm_tpm.txt


title: H2O-2

description:
TRANSCRIPTOMIC
H2O_FPKM.txt

value: petal


title: poly(A)-selection, jird, 3 dpi, b, SRX1539758

description:
bmalayi_counts.txt
bmalayi_tpm.txt

source_name: B. malayi taken from jirds 3 dpi

value: jird, 3 dpi


title: 48hpab_2


title: uninjured_2


title: poly(A)-depletion, jird, 20 dpi immature male, a, SRX1539754

description:
wbm_counts.txt
wbm_tpm.txt


title: H2O-1

description:
TRANSCRIPTOMIC
H2O_FPKM.txt

value: outer


title: poly(A)-selection, jird, 3 dpi, a, SRX1539755

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: poly(A)-enrichment


title: NAA-3

description:
TRANSCRIPTOMIC
NAA_FPKM.txt